breseq  version 0.29.0  revision 8f9c342918e4 mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Marginal read alignment evidence (highest frequency 20 of 45 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,890	0	C	A	64.7%	‑6.3 / 17.4	17	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	2,228,272	0	A	C	60.0%	7.3 / 14.1	15	pseudogene (338/1287 nt)	mdtQ	pseudogene; putative channel/filament proteins
*	NC_000913	213,341	0	A	G	58.6%	12.8 / 34.6	29	G337G (GGA→GGG)	tilS	tRNA(Ile)‑lysidine synthetase
*	NC_000913	1,222,233	0	G	A	56.5%	4.7 / 26.6	23	pseudogene (60/75 nt)	ycgH	pseudogene; putative ATP‑binding component of a transport system
*	NC_000913	4,332,791	0	A	C	55.6%	15.3 / 24.3	18	V161G (GTG→GGG)	basS	sensory histidine kinase in two‑component regulatory system with BasR
*	NC_000913	436,516	0	C	A	54.5%	8.7 / 28.4	23	Q295K (CAA→AAA)	thiL	thiamine monophosphate kinase
*	NC_000913	646,747	0	T	G	54.2%	28.3 / 36.9	24	T255P (ACC→CCC)	citG	2‑(5''‑triphosphoribosyl)‑3'‑dephosphocoenzyme‑A synthase
*	NC_000913	599,576	0	T	G	54.0%	38.8 / 57.9	37	V288G (GTG→GGG)	cusA	copper/silver efflux system, membrane component
*	NC_000913	3,733,280	0	T	A	53.3%	10.1 / 19.9	15	N360K (AAT→AAA)	xylG	D‑xylose ABC transporter dual domain ATPase
*	NC_000913	1,413,735	0	A	T	51.8%	14.5 / 42.5	27	Y2* (TAT→TAA)	ydaC	DUF1187 family protein, Rac prophage; putative double‑strand break reduction protein
*	NC_000913	3,206,435	0	C	T	50.0%	14.6 / 29.5	36	intergenic (‑179/‑28)	ttdR/ttdA	transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit
*	NC_000913	3,595,044	0	T	A	48.6%	26.5 / 19.2	35	Y146F (TAC→TTC)	livM	branched‑chain amino acid ABC transporter permease
*	NC_000913	898,598	0	T	A	48.0%	17.4 / 10.4	25	A27A (GCT→GCA)	rlmC	23S rRNA m(5)U747 methyltransferase, SAM‑dependent
*	NC_000913	753,125	0	T	A	46.2%	19.7 / 13.9	27	intergenic (‑330/+60)	ybgD/gltA	putative fimbrial‑like adhesin protein/citrate synthase
*	NC_000913	4,538,101	0	G	T	45.5%	53.0 / 15.9	33	T222N (ACC→AAC)	nanM	N‑acetylneuraminic acid mutarotase
*	NC_000913	4,287,719	0	T	A	44.8%	20.2 / 20.4	29	intergenic (‑348/‑45)	acs/nrfA	acetyl‑CoA synthetase/nitrite reductase, formate‑dependent, cytochrome
*	NC_000913	2,386,862	0	G	A	42.9%	28.2 / 18.4	28	intergenic (+31/‑72)	yfbL/yfbM	putative M28A family peptidase/DUF1877 family protein
*	NC_000913	2,628,625	0	A	C	42.9%	60.5 / 13.9	43	V105G (GTC→GGC)	yfgF	cyclic‑di‑GMP phosphodiesterase, anaerobic
*	NC_000913	3,206,444	0	T	A	42.9%	30.3 / 19.7	35	intergenic (‑188/‑19)	ttdR/ttdA	transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit
*	NC_000913	4,465,787	0	G	A	42.9%	36.5 / 15.8	35	R132C (CGC→TGC)	treB	trehalose‑specific PTS enzyme: IIB and IIC component

Marginal new junction evidence (sorted from low to high skew)
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	4542682 =	36 (1.050)	8 (0.250)	7/280	3.8	19.1%	intergenic (+49/‑433)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	4542996 =	34 (1.060)					intergenic (+363/‑119)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
*	?	NC_000913	= 4542690	34 (0.990)	5 (0.160)	5/280	4.7	13.3%	intergenic (+57/‑425)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	= 4542986	33 (1.030)					intergenic (+353/‑129)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)